Skip to main content
Glama

dpt

Perform Diffusion Pseudotime (DPT) analysis on single-cell RNA sequencing data to identify developmental trajectories and branchings using configurable parameters such as diffusion components and group size thresholds.

Instructions

Diffusion Pseudotime (DPT) analysis

Input Schema

NameRequiredDescriptionDefault
allow_kendall_tau_shiftNoIf a very small branch is detected upon splitting, shift away from maximum correlation in Kendall tau criterion to stabilize the splitting.
min_group_sizeNoDuring recursive splitting of branches, do not consider groups that contain less than min_group_size data points. If a float, refers to a fraction of the total number of data points.
n_branchingsNoNumber of branchings to detect.
n_dcsNoThe number of diffusion components to use.
neighbors_keyNoIf specified, dpt looks .uns[neighbors_key] for neighbors settings and uses the corresponding connectivities and distances.

Input Schema (JSON Schema)

{ "description": "Input schema for the Diffusion Pseudotime (DPT) tool.", "properties": { "allow_kendall_tau_shift": { "default": true, "description": "If a very small branch is detected upon splitting, shift away from maximum correlation in Kendall tau criterion to stabilize the splitting.", "title": "Allow Kendall Tau Shift", "type": "boolean" }, "min_group_size": { "default": 0.01, "description": "During recursive splitting of branches, do not consider groups that contain less than min_group_size data points. If a float, refers to a fraction of the total number of data points.", "exclusiveMinimum": 0, "maximum": 1, "title": "Min Group Size", "type": "number" }, "n_branchings": { "default": 0, "description": "Number of branchings to detect.", "minimum": 0, "title": "N Branchings", "type": "integer" }, "n_dcs": { "default": 10, "description": "The number of diffusion components to use.", "exclusiveMinimum": 0, "title": "N Dcs", "type": "integer" }, "neighbors_key": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "If specified, dpt looks .uns[neighbors_key] for neighbors settings and uses the corresponding connectivities and distances.", "title": "Neighbors Key" } }, "title": "DPTModel", "type": "object" }

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/huang-sh/scmcp'

If you have feedback or need assistance with the MCP directory API, please join our Discord server